MEDICAID AUDITORS FIND AGAINST STATE

New York State and the Federal Government are embroiled in a dispute over the state's claim to more than $40 million in Federal Medicaid funds.

A settlement is being negotiated, but New York officials say they fear they will not get the same favorable treatment from the Reagan Administration that New Jersey got last month.

An unreleased Federal audit review of New York State's facilities for the mentally retarded has found that the state improperly spent $17.8 million in Federal Medicaid funds, and has recommended that the money be recovered from the state.

The same audit by the regional office of the Inspector General of the United States Department of Health and Human Services identified $22.7 million more for possible recovery. New Jersey Misses Deadline

The office recommended in January that the funds be recovered. However, Secretary Richard S. Schweiker of the United States Department of Health and Human Services overruled his auditors and said last month that the funds should not be repaid.

Officials of Governor Carey's outgoing Democratic administration say they doubt they will receive the same favorable treatment as the new Republican administration of Governor Kean in New Jersey.

Richard J. McGowan, a spokesman for the Inspector General, described the New York audit review as ''extremely premature'' and said he would have no comment on it. Margaret McGraw, a spokesman for the State Office of Mental Retardation and Developmental Disabilities, also declined comment.

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However, Federal auditors who conducted the survey met with state officials on Wednesday in Albany to discuss the review and to explain why they were recommending a recovery of $40.5 million at a time when Federal Medicaid funds are being cut in Washington. Certification at Issue

Essentially, the auditors have said that New York was billing Medicaid for care provided in state facilities that were not certified as meeting Federal standards or in which billings exceeded certified patient levels.

For example, the audit said that from April 1, 1975, to Dec. 31, 1981, 11 of the state's 20 intermediate-care facilities for the mentally retarded claimed $17.8 million in Federal Medicaid funds for care in excess of their certified bed capacity. There was no allegation that the state billed Medicaid for care that was not rendered.

''Overall,'' the auditors reported, ''we have identified and developed findings which show improper billings to Medicaid totaling about $40.5 million in Federal funds.''

All told, the state spends nearly $1 billion a year caring for retarded and disabled clients. About half the expenditure is federally financed, and a recovery of funds of the size recommended by the regional auditors would have a serious impact on New York's program.

According to Federal health officials, the audits of New York and New Jersey were the first of a nationwide survey of the use of Medicaid funds.

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A version of this article appears in print on August 29, 1982, on Page 1001054 of the National edition with the headline: MEDICAID AUDITORS FIND AGAINST STATE. Order Reprints|Today's Paper|Subscribe